How many sub materials is recommended to have?
Also is it better to create one material with many sub-materials, or to have many materials which contain less sub-materials?

I would recommend you to have one material with multiple sub-materials. It will def. help you with performance! =)

You can use as many sub materials as your model(s) need.
Although for performance it shouldn't matter that much, they are still full materials, but have the ability to be indexed and referenced by the model for certain polys.

Efficient texture atlas' could improve performance though. For groups of objects that appear together a lot for example.